User:Karl E. Zahn/Sandbox RB69 1/palm-domain



The two-metal ion mechanism employed during the DNA pol catalytic cycle relies on coordination of divalent cations by conserved aspartate motifs in the palm domain. The palm domain of RB69 DNA pol (residues 383-468, 573-729) contains such motifs (LDFASLYPSI and DTDS) that are particular to family B DNA pols. Interestingly, the residue T622 in this sequence must obtain a high energy conformation in order to correctly orient the D621 and D623. This property is evident in Ramachandran plots of RB69 DNA pol where T622 is an obvious out-layer. L411 and D412 complete the coordination sphere of metal ion B.



A common strategy for crystallizing DNA polymerases in complex with both DNA and an incoming nucleoside triphosphate utilizes a dideoxy-terminated primer strand in the DNA molecule. Since the 3'-OH is absent, the reaction can not proceed following binding and alignment of the substrates. However, since the 3'-OH is required to complete contacts to the coordination sphere of metal ion A, complexes with chain terminated primers often illustrate perturbation or absence of this ion. Metal B is absent in the structure 2OZS.